Typical procedures for analyzing biological materials, such as nucleic acid, involve a variety of operations starting from raw material. These operations may include various degrees of cell purification, lysis, amplification or purification, and analysis of the resulting amplified or purified product.
As an example, in DNA-based blood tests the samples are often purified by filtration, centrifugation or by electrophoresis so as to eliminate all the non-nucleated cells. Then, the remaining white blood cells are lysed using chemical, thermal or biochemical means in order to liberate the DNA to be analyzed.
Next, the DNA is denatured by thermal, biochemical or chemical processes and amplified by an amplification reaction, such as PCR (polymerase chain reaction), LCR (ligase chain reaction), SDA (strand displacement amplification), TMA (transcription-mediated amplification), RCA (rolling circle amplification), and the like. The amplification step allows the operator to avoid purification of the DNA being studied because the amplified product greatly exceeds the starting DNA in the sample.
The procedures are similar if RNA is to be analyzed, but more emphasis is placed on purification or other means to protect the labile RNA molecule. RNA is usually copied into DNA (cDNA) and then the analysis proceeds as described for DNA.
Finally, the amplification product undergoes some type of analysis, usually based on sequence or size or some combination thereof. In an analysis by hybridization, for example, the amplified DNA is passed over a plurality of detectors made up of individual oligonucleotide probe fragments that are anchored, for example, on electrodes. If the amplified DNA strands are complementary to the probes, stable bonds will be formed between them and the hybridized probes can be read by observation by a wide variety of means, including optical, electrical, mechanical, magnetic or thermal means.
Other biological molecules are analyzed in a similar way, but typically molecule purification is substituted for amplification and detection methods vary according to the molecule being detected. For example, a common diagnostic involves the detection of a specific protein by binding to its antibody or by a specific enzymatic reaction. Lipids, carbohydrates, drugs and small molecules from biological fluids are processed in similar ways
The discussion herein is simplified by focusing on nucleic acid analysis, in particular DNA amplification, as an example of a biological molecule that can be analyzed using the devices of the invention. However, as described above, the invention can be used for any chemical or biological test.
The steps of nucleic acid analysis described above are currently performed using different devices, each of which presides over one part of the process. The use of separate devices decreases efficiency and increases cost, in part because of the required sample transfer between the devices. Another contributor to inefficiencies are the large sample sizes, required to accommodate sample loss between devices and instrument limitations. Most importantly, expensive, qualified operators are required to perform the analysis. For these reasons a fully integrated micro-device would be preferred.
For performing treatment of fluids, integrated microreactors of semiconductor material are already known.
For example, publication EP 161985 (corresponding to U.S. Pat. No. 6,710,311 et seq.) describes a microreactor and the respective manufacturing process suitable for DNA-amplification processes.
According to this process, a substrate of monocrystalline silicon is etched in TMAH to form a plurality of thin channels that are then coated with a material inhibiting epitaxial growth; then a monocrystalline epitaxial layer is grown on top of the substrate and of the channels. The epitaxial layer closes at the top the buried channels and forms, together with the substrate, a semiconductor body. The surface of the semiconductor body is then covered with an insulating layer; heating and sensing elements are formed on the insulating layer; inlet and outlet apertures are formed through the insulating layer and the semiconductor body and connect the surface of the structure so obtained with the buried channels. Then, a covering structure accommodating an inlet and an outlet reservoir is formed or bonded on the structure accommodating the buried channels.
According to a different solution, disclosed e.g. in publication EP1193214 (corresponding to U.S. Pat. No. 6,770,471) for manufacturing buried cavities, the channels are etched using a grid-like mask having a particular orientation. The grid-like mask is made of polysilicon completely surrounded by nitride; after channel etching, the nitride is removed and a pseudo-epitaxial layer is grown from the mask polysilicon. In the alternative, in case of reduced width channels, the grid-like mask is made of insulating material, and the pseudo-epitaxial layer is directly grown thereon, after forming the channels.
According to a further different embodiment, for manufacturing buried cavities, the channels are etched using a grid-like mask of silicon oxide and nitride and are closed upwardly by depositing a polysilicon layer that collects around the grid-like mask and by oxidizing the polysilicon layer. This embodiment, similar to the one described e.g. in Italian patent application TO2002A000808 filed on Sep. 17, 2002 and publication EP1400600 filed on Sep. 17, 2003 (corresponding to publication US2004132059 filed Sep. 16, 2003) in the name of the same applicant regarding a fully integrated microreactor system, containing pretreatment channels, lysis chambers, amplification channels, heaters, detectors, and a micropump, is described hereinbelow with reference to FIGS. 1-5.
Initially, FIG. 1, a wafer 10 including a substrate 1 of semiconductor material, e.g. silicon, is masked to form channels. To this end, a pad oxide layer 3 (with a thickness of, e.g., 550 nm) and a nitride layer 4 (with a thickness of, e.g., 540 nm) are deposited on a surface 5 of the substrate 1 and then photolithographically defined to form a hard mask 2. The hard mask 2 has groups of openings 6, e.g. with a square, rectangular or lozenge shape.
Then, FIG. 2, using the hard mask 2, the substrate 1 is etched using tetramethylammoniumhydroxide (TMAH), forming channels 13.
Next, FIG. 3, a polysilicon layer 14 (with a thickness of, e.g., 450 nm) is deposited and coats the surface of the hard mask 2 and the walls 13a of the channels 13. In addition, the polysilicon layer 14 completely surrounds the hard mask 2, covering also the lateral sides and the lower side.
The polysilicon layer 14 is then thermally oxidized (FIG. 4); during oxidation, the polysilicon increases its volume so as to close the openings 6 and to form a silicon oxide layer 15 of about 2 μm. Moreover, an oxide layer 16 is formed also on the walls 13a of the channels 13.
Thereafter, a seed layer 17 of polysilicon is deposited (FIG. 5) and removed, together with the oxide layer 15, the nitride layer 4 and the pad oxide layer 3, outside the region of the channels 13; and a pseudo-epitaxial layer 18 is grown (e.g. for a thickness of 10 μm). The pseudo-epitaxial layer 18 is polycrystalline above the seed layer and monocrystalline on the substrate 1. The surface of the pseudo-epitaxial layer 18 is then thermally oxidized, forming an upper oxide layer 19, obtaining the structure of FIG. 5.
Then the process continues with the other steps for forming heating elements, inlets/outlets, sensing elements and an upper layer having input/output reservoirs on top of the inlets/outlets.
The above solution has proven satisfactorily, but is suitable only when the microreactor is to be used for treating small amounts of liquids. In fact, the height of the channels is strictly dependent on the width thereof, due to the TMAH etching technique, and the width of the channel cannot be increased beyond a preset value (about 200 μm) because, due to its manufacturing technique, the oxide diaphragm is subject to stresses and may break easily. Thus, the volume of each channel is limited and when high volumes of liquids are to be treated, it is necessary to increase the number of channels. However such solution is disadvantageous, since it involves a corresponding increase in the dimensions of the microreactor and can lead to uneven treatment conditions across the microreactor.